You'll have to be more specific and break it down a little more.
The most important question;
What are you trying to do, in the big picture? What is this for?
And then a torrent of smaller questions, based on exactly what you've described;
What do you mean by "merge"? How are you planning on doing a "merge"?
When you say "two input files into a third file", do you mean that you want a third file that is exactly the length of the first two files combined, and the contents of that "third file" will be the contents of the first file, immediately followed by the contents of the second file?
Where is this third file going to be stored? Is this file going to be saved to disk, or do you want it to be done entirely in memory?
C++ has
file streams to work with files of every kind, you should look into that.
It would help to pick up a book on C++ so that you can have all this information laid out for you, the
C++ Primer is a popular choice, and Scott Meyers recently released another book in the "Effective C++" series,
Effective Modern C++. I would recommend picking up those this weekend.